[BioC] getBioC()

Claudio Lottaz Claudio.Lottaz at molgen.mpg.de
Wed Apr 30 12:36:46 MEST 2003


Hi all,
Does anybody know what goes wrong when I receive the message

   Error: evaluation is nested too deeply: infinite recursion?

during installation with getBioC() using getAllDeps=T? See the log 
attached for more details.
Thanks
Claudio


Jeff Gentry wrote:

>Hello ...
>
>The latest version of getBioC() (1.2.28) involves a change to its
>parameters and not just internal improvements.  This will not affect most
>users, but for those who it will affect:
>
>- The 'isDevel' and 'version' arguments are no longer present.
>- A 'relLevel' argument has been added, which can be one of 'release',
>'devel', 'contrib', and 'release1.0'.  The default is 'release', which
>will always point ot the current release (currently 1.1).  The 'contrib'
>option will install/update packages that have been contributed by the
>Bioconductor user community.
>
>-Jeff
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
>  
>


-- 
----------------------------------------------------------------------
Claudio Lottaz
Max Planck Institute for Molecular Genetics
Computational Molecular Biology Department
Ihnestrasse 73, D-14195 Berlin (Germany)

phone: +49 (0)30 8413 1177
  fax: +49 (0)30 8413 1176
  www: http://www.molgen.mpg.de/~lottaz

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> source('http://www.bioconductor.org/getBioC.R')
> .libPaths('/project/gene_expression/lib/R/alpha/devel')
> getBioC(libName='all',destdir='/project/gene_expression/lib/R/alpha/devel',relLevel='devel',getAllDeps=T)
Running getBioC version 1.2.28....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R

Please direct any concerns or questions to bioconductor at stat.math.ethz.ch.

[1] "Installing reposTools ..."
Creating a new generic function for "summary" in package 
reposTools 

Synching your local package management information ...
Packages which have been added/updated:
	AnnBuilder
	Biobase
	DynDoc
	ROC
	Ruuid
	SAGElyzer
	affy
	affycomp
	annotate
	dbTools
	edd
	genefilter
	geneplotter
	golubEsets
	graph
	hexbin
	makecdfenv
	marrayClasses
	marrayInput
	marrayNorm
	marrayPlots
	marrayTools
	multtest
	pubRepo
	tkWidgets
	vsn
	

Packages which have been removed:
	KernSmooth
	MASS
	base
	boot
	class
	cluster
	ctest
	eda
	foreign
	grid
	lattice
	lqs
	methods
	mgcv
	modreg
	mva
	nlme
	nls
	nnet
	rpart
	spatial
	splines
	stepfun
	survival
	tcltk
	tools
	ts
	

Packages which have been added/updated:
	KernSmooth
	MASS
	base
	boot
	class
	cluster
	ctest
	eda
	foreign
	grid
	lattice
	lqs
	methods
	mgcv
	modreg
	mva
	nlme
	nls
	nnet
	rpart
	spatial
	splines
	stepfun
	survival
	tcltk
	tools
	ts
	

Note: No specified download type, defaulting to Source 
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[1] "Attempting to download reposTools from http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing reposTools"
* Installing *source* package 'reposTools' ...
** R
** data
** inst
** help
 >>> Building/Updating help pages for package 'reposTools'
     Formats: text html latex example 
  ReposEntry-class                  text    html    latex   example
  ReposList-class                   text    html    latex   example
  VersionNumber-class               text    html    latex   example
  buildPkgInfo                      text    html    latex   example
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  buildReposEntry                   text    html    latex   example
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  unpackExtractPkgDESC              text    html    latex   example
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  winConvertSourceRepos             text    html    latex   example
* DONE (reposTools)

* DONE (INSTALL)
[1] "Installation complete"
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[1] "Attempting to download widgetTools from http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing widgetTools"
* Installing *source* package 'widgetTools' ...
** R
** inst
** help
 >>> Building/Updating help pages for package 'widgetTools'
     Formats: text html latex example 
  basicPW-class                     text    html    latex   example
  button                            text    html    latex   example
  makeViewer                        text    html    latex   example
  widget-class                      text    html    latex   example
  widgetView-class                  text    html    latex   example
  writeText                         text    html    latex   example
* DONE (widgetTools)

* DONE (INSTALL)
[1] "Installation complete"
Note: No specified download type, defaulting to Source 
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